There are several lessons or morals to be learned, as indirectly "stated" as they may be. One is that acceptance of others helps one find self-acceptance as well. For example, when Christopher forgives his father for having killed the neighbour's dog and simulated his mother's death for the simple reason of convenience, he does not bear a grudge but accepts his father's confession of fault. Father and son start sharing activites together which they had not done before, and Christopher learns to be more optimistic about his future, now that the shadows of an uncertain past have been dissipated.

Another lesson is that problems can be an opportunity to learn and grow. Christopher would have never ventured beyond the perimeter of his own neighbourhood had he not discovered letters from his mother and gone to London in search of her. He learns how to cope with new and unfamiliar experiences, such as riding on a train and not getting lost and finding his mother alive and well after having thought she had died at hospital.

Another theme which is an offshoot of the previously mentioned one is that a person can turn a weakness into a strength. Christopher's autism makes him uncompromizingly blunt, but it his his straightforward nature which helps his father escape the snare of lies and dissimulation. Mr Boone learns to be an honest person again after a "snowball effect" of pretention.

According to the author, the purpose of this book was not to moralize but to expose the personality of a marginal type fragilized by both his handicap and his life experience. Christopher is not an endearing character, he is not loveable or even that likable, but the reader becomes "engaged" just the same. The reader lets himself, much as Alice, plunge into a world where the rules and usual code of behaviour no longer apply. He learns to "think different" and see the world from a perspective other than his own, and this is a lesson in itself.

Christopher finds it impossible to identify with other people, and as a result lives in his own little world. The people he meets are rude and inconsiderate regarding his disability. He finds other people weird and confusing, and prefers to be on his own. His disconnection from other people is also physical, whereby he hates being touched and is even given a police caution for hitting a policeman who touched him on the arm. Additionally, the author makes Christopher stand out through his hobbies and his superstitions. He physically cannot lie, as when he thinks of one thing that might have happened instead, a million other possibilities crowd into his head and he feels overwhelmed.

Through this book, the author questions how much parenting impacts one's identity. Christopher has little understanding of “love”, and instead cares more for dogs and his pet rat Toby. He detaches himself from his parents very easily -not too bothered when describing his mum's “death” and running away from his dad. He refers to them as “mother” and “father”, which aren’t very affectionate terms. Furthermore, he doesn’t realize the impact he has on other people’s relationships, as both his parents and his mum and her boyfriend split up on account of him.

One lesson is that there are many ways to see and interpret the world and there are many ways to live a human life. Many have the idea that there is a "norm" about how we should live, and how we should relate to others. Christopher Boone exemplifies one way to interact with the world. His descriptions about what he sees, for example his analysis of the ad for Malayasia, provide insight into the assumptions our "appropriate" worlds makes about human existence, values and truth.

Given a distressful condition, Christopher manages to relate to others and to experience the human emotions of fear, excitment, worry, courage,interest, self-satisfaction and empathy (especially for Wellington and Toby). He relates to his teacher at school and respects what she has taught him. Granted, his way of relating is not how most people experience it, but he does interact with others. At the end of the novel he is able to begin to see is father as trustworthy and to reconcile. Christopher does love his father and he learns that the ordered world he wants sometimes does not happen. Christopher has learned to begin to adapt, one of the hardest things for people with autism. And best of all, the novel ends with his hopes for his future. Christopher does not see anything wrong with himself, and this is the best lesson of all.